Merge pull request #178 from BryanGuillaume/new_release_2.2.1

Release SwE Version 2.2.1

.travis.yml

@@ -1,26 +1,26 @@
 language: python
 # use container-based infrastructure
 sudo: required
-services: 
+services:
   - docker
-cache: 
+cache:
   timeout: 1000
   directories:
   - test/data
 python:
   - "3.5"
 bundler_args: --retry 9
 # command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: 
- # Install git-lfs 
+install:
+ # Install git-lfs
  - cd ..
  - curl -sLo - https://github.com/github/git-lfs/releases/download/v1.4.1/git-lfs-linux-amd64-1.4.1.tar.gz | tar xzvf -
  - export PATH=$PATH:`pwd`/git-lfs-1.4.1
- - git lfs install  
+ - git lfs install
  # Download data.
  - cd SwE-toolbox/test/data
  - if ! [ -d .git ]; then git clone https://github.com/NISOx-BDI/SwE-toolbox-testdata.git .; fi
- # Delete any previous changes (retry because lfs might download files) 
+ # Delete any previous changes (retry because lfs might download files)
  - git checkout master
  - travis_retry git reset --hard origin/master
  # A second time to allow for 3 more retries as "--retry 9" does not seem to be
@@ -31,7 +31,7 @@ jobs:
   include:
     # Each '-' with the same indentation as this comment is a job that is run in parallel in the
     # results generation stage.
-    - stage: Results generation 
+    - stage: Results generation
       env:
       - testname='p_vox_t_nii'
       script:
@@ -41,7 +41,7 @@ jobs:
       - testname='p_vox_f_nii'
       script:
       - did=$(sudo docker run -ti -d --rm -v `pwd`:/swe cmaumet/octave-spm)
-      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'vox', 'f', 'nii')"   
+      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'vox', 'f', 'nii')"
     - env:
       - testname='wb_vox_t_nii'
       script:
@@ -66,7 +66,7 @@ jobs:
       - testname='wb_tfce_t_nii'
       script:
       - did=$(sudo docker run -ti -d --rm -v `pwd`:/swe cmaumet/octave-spm)
-      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('wb', 'tfce', 't', 'nii')"          
+      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('wb', 'tfce', 't', 'nii')"
     - env:
       - testname='wb_tfce_f_nii'
       script:
@@ -81,7 +81,7 @@ jobs:
       - testname='p_dat_f_mat'
       script:
       - did=$(sudo docker run -ti -d --rm -v `pwd`:/swe cmaumet/octave-spm)
-      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'dat', 'f', 'mat')"   
+      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'dat', 'f', 'mat')"
     - env:
       - testname='wb_dat_t_mat'
       script:
@@ -111,7 +111,7 @@ jobs:
       - testname='p_dpx_f_gii'
       script:
       - did=$(sudo docker run -ti -d --rm -v `pwd`:/swe cmaumet/octave-spm)
-      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'dpx', 'f', 'gii')"   
+      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'dpx', 'f', 'gii')"
     - env:
       - testname='wb_dpx_t_gii'
       script:
@@ -141,7 +141,7 @@ jobs:
       - testname='p_dpx_f_cii'
       script:
       - did=$(sudo docker run -ti -d --rm -v `pwd`:/swe cmaumet/octave-spm)
-      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'dpx', 'f', 'cii')"   
+      - sudo docker exec -t -i $did octave --no-window-system --eval "addpath('/swe/test');runTest('p', 'dpx', 'f', 'cii')"
     - env:
       - testname='wb_dpx_t_cii'
       script:
@@ -166,6 +166,6 @@ before_install:
  # Update docker version
  - sudo apt-get update
  - sudo apt-get -y -o Dpkg::Options::="--force-confnew" install docker-ce
- - git config --global user.name "TravisCI" 
+ - git config --global user.name "TravisCI"
  - git config --global user.email "[email protected]"
- - docker pull cmaumet/octave-spm 
+ - docker pull cmaumet/octave-spm

@swe_DataType/display.m

@@ -1,9 +1,9 @@
 function display(obj)
-	% Display a swe_DataType object
-	% =========================================================================
+  % Display a swe_DataType object
+  % =========================================================================
   % Bryan Guillaume
   % Version Info:  $Format:%ci$ $Format:%h$
-	
-	display(get(obj));
-	
-end
+
+  display(get(obj));
+
+end

@swe_DataType/eq.m

@@ -1,9 +1,9 @@
 function out = eq(a,b)
-	% Overload the '==' operator for we_DataType objects
+  % Overload the '==' operator for we_DataType objects
   % =========================================================================
   % Bryan Guillaume
-	% Version Info:  $Format:%ci$ $Format:%h$
-
-	out = strcmp(a.value, b.value);
+  % Version Info:  $Format:%ci$ $Format:%h$
 
-end
+  out = strcmp(a.value, b.value);
+
+end

@swe_DataType/get.m

@@ -1,9 +1,9 @@
 function out = get(obj)
-	% Get a swe_DataType object
-	% =========================================================================
+  % Get a swe_DataType object
+  % =========================================================================
   % Bryan Guillaume
   % Version Info:  $Format:%ci$ $Format:%h$
-
-	out = obj.value;
 
-end
+  out = obj.value;
+
+end

@swe_DataType/swe_DataType.m

@@ -5,9 +5,9 @@
   % =========================================================================
   % Bryan Guillaume
   % Version Info:  $Format:%ci$ $Format:%h$
-  
+
   availableDataTypes = {'Nifti', 'Gifti', 'Cifti', 'Mat', 'VolumeMat', 'SurfaceMat'};
-  
+
   if nargin == 0
     error( "swe_DataType cannot be initialized empty; choose from 'Nifti', 'Gifti', 'Cifti', 'Mat', 'VolumeMat' or 'SurfaceMat'.");
   end
@@ -17,7 +17,7 @@
   end
 
   obj.value = dataType;
-  
+
   obj = class(obj, 'swe_DataType');
 
-end
+end

@swe_cifti/Contents.m

@@ -18,59 +18,59 @@
 % dat.dim     = [64 64 32];
 % dat.dtype  = 'FLOAT64-BE';
 % dat.offset  = ceil(348/8)*8;
-% 
+%
 % % alternatively:
 % % dat = file_array( 'junk.nii',dim,dtype,off,scale,inter)
-% 
+%
 % disp(dat)
-% 
+%
 % % Create an empty NIFTI structure
 % N = nifti;
-% 
+%
 % fieldnames(N) % Dump fieldnames
-% 
+%
 % % Creating all the NIFTI header stuff
 % N.dat = dat;
 % N.mat = [2 0 0 -110 ; 0 2 0 -110; 0 0 -2 92; 0 0 0 1];
 % N.mat_intent = 'xxx'; % dump possibilities
 % N.mat_intent = 'Scanner';
 % N.mat0 = N.mat;
 % N.mat0_intent = 'Aligned';
-% 
+%
 % N.diminfo.slice = 3;
 % N.diminfo.phase = 2;
 % N.diminfo.frequency = 2;
-% N.diminfo.slice_time.code='xxx'; % dump possibilities 
+% N.diminfo.slice_time.code='xxx'; % dump possibilities
 % N.diminfo.slice_time.code = 'sequential_increasing';
 % N.diminfo.slice_time.start = 1;
 % N.diminfo.slice_time.end = 32;
 % N.diminfo.slice_time.duration = 3/32;
-% 
+%
 % N.intent.code='xxx' ; % dump possibilities
 % N.intent.code='FTEST'; % or N.intent.code=4;
 % N.intent.param = [4 8];
-% 
+%
 % N.timing.toffset = 28800;
 % N.timing.tspace=3;
 % N.descrip = 'This is a NIFTI-1 file';
 % N.aux_file='aux-file-name.txt';
 % N.cal = [0 1];
-% 
+%
 % create(N); % Writes hdr info
-% 
+%
 % dat(:,:,:)=0; % Write out the data as all zeros
-% 
+%
 % [i,j,k] = ndgrid(1:64,1:64,1:32);
 % dat(find((i-32).^2+(j-32).^2+(k*2-32).^2 < 30^2))=1; % Write some ones in the file
 % dat(find((i-32).^2+(j-32).^2+(k*2-32).^2 < 15^2))=2;
-% 
-% 
+%
+%
 % % displaying a slice
 % imagesc(dat(:,:,12));colorbar
-% 
+%
 % % get a handle to 'junk.nii';
 % M=nifti('junk.nii');
-% 
+%
 % imagesc(M.dat(:,:,12));
 %
 % _______________________________________________________________________

@swe_cifti/create.m

@@ -13,21 +13,21 @@ function create(obj,wrt)
 
 
 for i=1:numel(obj)
-    
+
     o = obj(i);
-    
+
     if ~isa(o.dat,'file_array'), error('Data must be a file_array.'); end
-    
+
     fname = o.dat.fname;
     if isempty(fname), error('No filename to write to.'); end
-    
+
     %-Write NIFTI header
     sts = write_hdr_raw(fname, o.hdr, o.dat.dtype(end-1)=='B');
     if ~sts, error('Unable to write header for "%s".',fname); end
-    
+
     %-Write extra information
     write_extras(fname,o.extras);
-    
+
     %-Create an empty image file if necessary
     if nargin>1 && any(wrt==1)
         [pth,nam] = fileparts(fname);
@@ -37,8 +37,8 @@ function create(obj,wrt)
             ext = '.img';
         end
         o.dat.fname = fullfile(pth,[nam ext]);
-        
+
         initialise(o.dat);
     end
-    
+
 end

@swe_cifti/subsasgn.m

@@ -27,7 +27,7 @@
     if length(subs)>1
         t    = subsref(objs,subs(1));
         % A lot of this stuff is a little flakey, and may cause Matlab to bomb.
-        % 
+        %
         %if numel(t) ~= nargin-2,
         %    error('The number of outputs should match the number of inputs.');
         %end;

@swe_cifti/subsref.m

@@ -86,7 +86,7 @@
             if s
                 d = findindict(s,'units');
                 if ~isempty(d)
-                    t = diag([d.rescale*[1 1 1] 1])*t; 
+                    t = diag([d.rescale*[1 1 1] 1])*t;
                 end
             end
 
@@ -151,12 +151,12 @@
                 se = double(h.slice_end)+1;
                 ss = max(ss,1);
                 se = min(se,double(h.dim(t.slice+1)));
-                
+
                 sd = double(h.slice_duration);
                 s  = double(bitand(h.xyzt_units,24));
                 d  = findindict(s,'units');
                 if d.rescale, sd = sd*d.rescale; end
-                
+
                 ns       = (se-ss+1);
                 d = findindict(sc,'sliceorder');
                 if isempty(d)

@swe_cifti/swe_cifti.m

@@ -20,7 +20,7 @@
   case {1, 2}
       if isa(varargin{1},'swe_cifti')
           h = varargin{1};
-          
+
       elseif ischar(varargin{1})
           if size(varargin{1},1)>1
               h = swe_cifti(cellstr(varargin{1}));
@@ -75,7 +75,7 @@
           h     = class(h,'swe_cifti');
 
       elseif isstruct(varargin{1})
-        
+
           h     = struct('hdr', varargin{1}.hdr,...
                          'dat', varargin{1}.dat,...
                          'extras', varargin{1}.extras);
@@ -92,8 +92,8 @@
       else
           error('Don''t know what to do yet.');
       end
-      
+
   otherwise
       error('Don''t know what to do yet.');
   end
-end
+end